TheVirtualBrain:

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Source code for tvb.config.init.initializer

# -*- coding: utf-8 -*-
#
#
# TheVirtualBrain-Framework Package. This package holds all Data Management, and 
# Web-UI helpful to run brain-simulations. To use it, you also need do download
# TheVirtualBrain-Scientific Package (for simulators). See content of the
# documentation-folder for more details. See also http://www.thevirtualbrain.org
#
# (c) 2012-2022, Baycrest Centre for Geriatric Care ("Baycrest") and others
#
# This program is free software: you can redistribute it and/or modify it under the
# terms of the GNU General Public License as published by the Free Software Foundation,
# either version 3 of the License, or (at your option) any later version.
# This program is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
# PARTICULAR PURPOSE.  See the GNU General Public License for more details.
# You should have received a copy of the GNU General Public License along with this
# program.  If not, see <http://www.gnu.org/licenses/>.
#
#
#   CITATION:
# When using The Virtual Brain for scientific publications, please cite it as follows:
#
#   Paula Sanz Leon, Stuart A. Knock, M. Marmaduke Woodman, Lia Domide,
#   Jochen Mersmann, Anthony R. McIntosh, Viktor Jirsa (2013)
#       The Virtual Brain: a simulator of primate brain network dynamics.
#   Frontiers in Neuroinformatics (7:10. doi: 10.3389/fninf.2013.00010)
#
#

"""
.. moduleauthor:: Lia Domide <lia.domide@codemart.ro>
"""
from datetime import datetime
import shutil
import threading

from tvb.adapters.datatypes.db import DATATYPE_REMOVERS
from tvb.basic.logger.builder import get_logger
from tvb.basic.profile import TvbProfile
from tvb.config import VIEW_MODEL2ADAPTER
from tvb.config.init.datatypes_registry import populate_datatypes_registry
from tvb.config.init.introspector_registry import IntrospectionRegistry
from tvb.config.init.model_manager import initialize_startup, reset_database
from tvb.core import removers_factory
from tvb.core.code_versions.code_update_manager import CodeUpdateManager
from tvb.core.entities.file.files_update_manager import FilesUpdateManager
from tvb.core.entities.model.model_operation import Algorithm, AlgorithmCategory
from tvb.core.entities.model.model_project import User, ROLE_ADMINISTRATOR
from tvb.core.entities.storage import dao, SA_SESSIONMAKER
from tvb.core.entities.storage.session_maker import build_db_engine
from tvb.core.neotraits.db import Base
from tvb.core.services.project_service import initialize_storage
from tvb.core.services.settings_service import SettingsService
from tvb.core.services.user_service import UserService


[docs]def reset(): """ Service Layer for Database reset. """ reset_database()
[docs]def command_initializer(persist_settings=True, skip_import=False): if persist_settings and TvbProfile.is_first_run(): settings_service = SettingsService() settings = {} # Save default settings for key, setting in settings_service.configurable_keys.items(): settings[key] = setting['value'] settings_service.save_settings(**settings) TvbProfile.set_profile(TvbProfile.COMMAND_PROFILE) # Build new db engine in case DB URL value changed new_db_engine = build_db_engine() SA_SESSIONMAKER.configure(bind=new_db_engine) # Initialize application initialize(skip_import)
[docs]def initialize(skip_import=False, skip_updates=False): """ Initialize when Application is starting. Check for new algorithms or new DataTypes. """ SettingsService().check_db_url(TvbProfile.current.db.DB_URL) # Initialize DB is_db_empty = initialize_startup() # Create Projects storage root in case it does not exist. initialize_storage() # Populate DB algorithms, by introspection start_introspection_time = datetime.now() # Introspection is always done, even if DB was not empty. introspector = Introspector() introspector.introspect() to_invalidate = dao.get_non_validated_entities(start_introspection_time) for entity in to_invalidate: entity.removed = True dao.store_entities(to_invalidate) if not TvbProfile.is_first_run() and not skip_updates: # Create default users. if is_db_empty: dao.store_entity( User(TvbProfile.current.web.admin.SYSTEM_USER_NAME, TvbProfile.current.web.admin.SYSTEM_USER_NAME, None, None, True, None)) UserService().create_user(username=TvbProfile.current.web.admin.ADMINISTRATOR_NAME, display_name=TvbProfile.current.web.admin.ADMINISTRATOR_DISPLAY_NAME, password=TvbProfile.current.web.admin.ADMINISTRATOR_PASSWORD, email=TvbProfile.current.web.admin.ADMINISTRATOR_EMAIL, role=ROLE_ADMINISTRATOR, skip_import=skip_import) # In case actions related to latest code-changes are needed, make sure they are executed. CodeUpdateManager().run_all_updates() # In case the H5 version changed, run updates on all DataTypes thread = None if TvbProfile.current.version.DATA_CHECKED_TO_VERSION < TvbProfile.current.version.DATA_VERSION: thread = threading.Thread(target=FilesUpdateManager().run_all_updates) thread.start() # Clean tvb-first-time-run temporary folder, as we are no longer at the first run: shutil.rmtree(TvbProfile.current.FIRST_RUN_STORAGE, True) return thread
[docs]class Introspector(object): def __init__(self): self.introspection_registry = IntrospectionRegistry() self.logger = get_logger(self.__class__.__module__)
[docs] def introspect(self): self._ensure_datatype_tables_are_created() populate_datatypes_registry() for algo_category_class in IntrospectionRegistry.ADAPTERS: algo_category_id = self._populate_algorithm_categories(algo_category_class) self._populate_algorithms(algo_category_class, algo_category_id) removers_factory.update_dictionary(DATATYPE_REMOVERS)
@staticmethod def _ensure_datatype_tables_are_created(): session = SA_SESSIONMAKER() Base.metadata.create_all(bind=session.connection()) session.commit() session.close() @staticmethod def _populate_algorithm_categories(algo_category): algo_category_instance = dao.filter_category(algo_category.category_name, algo_category.rawinput, algo_category.display, algo_category.launchable, algo_category.order_nr) if algo_category_instance is not None: algo_category_instance.last_introspection_check = datetime.now() algo_category_instance.removed = False else: algo_category_instance = AlgorithmCategory(algo_category.category_name, algo_category.launchable, algo_category.rawinput, algo_category.display, algo_category.defaultdatastate, algo_category.order_nr, datetime.now()) algo_category_instance = dao.store_entity(algo_category_instance) return algo_category_instance.id def _populate_algorithms(self, algo_category_class, algo_category_id): for adapter_class in self.introspection_registry.ADAPTERS[algo_category_class]: try: if not adapter_class.can_be_active(): self.logger.warning("Skipped Adapter(probably because MATLAB not found):" + str(adapter_class)) stored_adapter = Algorithm(adapter_class.__module__, adapter_class.__name__, algo_category_id, adapter_class.get_group_name(), adapter_class.get_group_description(), adapter_class.get_ui_name(), adapter_class.get_ui_description(), adapter_class.get_ui_subsection(), datetime.now()) adapter_inst = adapter_class() adapter_form = adapter_inst.get_form() required_datatype = adapter_form.get_required_datatype() if required_datatype is not None: required_datatype = required_datatype.__name__ filters = adapter_form.get_filters() if filters is not None: filters = filters.to_json() stored_adapter.required_datatype = required_datatype stored_adapter.datatype_filter = filters stored_adapter.parameter_name = adapter_form.get_input_name() stored_adapter.outputlist = str(adapter_inst.get_output()) inst_from_db = dao.get_algorithm_by_module(adapter_class.__module__, adapter_class.__name__) if inst_from_db is not None: stored_adapter.id = inst_from_db.id stored_adapter = dao.store_entity(stored_adapter, inst_from_db is not None) view_model_class = adapter_form.get_view_model() VIEW_MODEL2ADAPTER[view_model_class] = stored_adapter adapter_class.stored_adapter = stored_adapter except Exception: self.logger.exception("Could not introspect Adapters file:" + adapter_class.__module__)